Phosphorylation in Protein-Protein Binding: Effect on Stability and Function  Hafumi Nishi, Kosuke Hashimoto, Anna R. Panchenko  Structure  Volume 19, Issue 12, Pages 1807-1815 (December 2011) DOI: 10.1016/j.str.2011.09.021 Copyright © 2011 Elsevier Ltd Terms and Conditions

Structure 2011 19, 1807-1815DOI: (10.1016/j.str.2011.09.021) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Probability Density Function of the Fraction of Phosphosites in Protein Complexes and on Binding Interfaces for Homooligomers and Heterooligomers Homooligomers (A) had 308 phosphosites in proteins and 111 on interfaces, and heterooligomers (B) had 290 phosphosites in proteins and 160 on interfaces. The difference between the mean values of these distributions is significant (p value = 2e-16 for both homooligomers and heterooligomers by Wilcoxon rank-sum test). Inset: curves for permanent homooligomers are shown in red, strong transient homooligomers are shown in orange, and weak transient homooligomers are shown in green. The distributions are smoothed by the Gaussian kernel density estimation. See also Tables S1 and S2. Structure 2011 19, 1807-1815DOI: (10.1016/j.str.2011.09.021) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Probability Density Function of the Change in Binding Energy upon Phosphorylation for Interfacial Ser, Thr, and Tyr (ΔΔΔGp) Curves for homooligomers (n = 74 phosphosites on interfaces) are shown in pink; curves for heterooligomers (n = 104) are shown in blue. Note that ΔΔΔGp was calculated only for dimers due to the limitations of the program. The distribution is shifted toward positive values (p value = 2e-16). Inset: permanent homooligomers are shown in red, strong transient homooligomers are shown in orange, and weak transient homooligomers are shown in green. The distributions are smoothed by the Gaussian kernel density estimation. Structure 2011 19, 1807-1815DOI: (10.1016/j.str.2011.09.021) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 Probability Density Function of the Conservation Score Calculated for Phosphorylation Sites on Binding Interfaces Zero conservation score corresponds to the same amount of evolutionary conservation as the mean conservation of the protein family. (A) For homooligomers, conservation of phosphorylation sites (n = 275 phosphosites on interfaces) is shown in red and conservation of nonphosphorylation sites (n = 2773) is shown in purple. (B) For heterooligomers, conservation of phosphorylation sites (n = 521) is shown in blue and conservation of nonphosphorylation sites (n = 5559) is shown in green. The conservation distribution for phosphosites is significantly shifted toward positive values compared to conservation of interfacial nonphosphosites for all complexes, and for heterooligomers in particular (p value = 0.018 for all and p value = 0.016 for heterooligomers). The distributions are smoothed by the Gaussian kernel density estimation. See also Figure S3. Structure 2011 19, 1807-1815DOI: (10.1016/j.str.2011.09.021) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 4 Phosphorylation in Smad1 and Smad2 Complexes (A) Superposition of Smad2 structure (PDB ID: 1khx; yellow) and phosphorylated model of Smad1 generated by FoldX (based on 1khu; individual subunits are shown in magenta, green, and blue). Phosphorylated Ser462, Ser463, and Ser465 are colored in red. (B) C-terminal loops of three subunits of phosphorylated Smad1 and Smad2. Colors of the subunits are the same as in (A), and phosphate groups are depicted in the same color as subunits. Structure 2011 19, 1807-1815DOI: (10.1016/j.str.2011.09.021) Copyright © 2011 Elsevier Ltd Terms and Conditions